Extended Data Table 1. Cryo-EM data collection, refinement and validation statistics.

Note: Atomic model refinement with state E_A map was done only for the CP and ATPase using part of the full atomic model from state E_A1. The final refined atomic model, 6MSB, includes the model components of CP and ATPase refined from the combined E_A map and the rest of holoenzyme from the E_A1 map. 5VFO was only used for the CP component for the initial atomic model of E_D2.

	EA (EMDB-9215) (PDB 6MSB)	EA1 (EMDB-9216,9223) (PDB 6MSB)	EA2 (EMDB-9217,9224) (PDB 6MSD)	EB (EMDB-9218,9225) (PDB 6MSE)	EC1 (EMDB-9219,9226) (PDB 6MSG)	EC2 (EMDB-9220,9227) (PDB 6MSH)	ED1 (EMDB-9221,9228) (PDB 6MSJ)	ED2 (EMDB-9222,9229) (PDB 6MSK)
Data collection and processing
Magnification	105,000	105,000	105,000	105,000	105,000	105,000	105,000	105,000
Voltage (kV)	300	300	300	300	300	300	300	300
Electron exposure (e–/Å2)	44	44	44	44	44	44	44	44
Defocus range (μm)	−0.6 to −3.5	−0.6 to −3.5	−0.6 to −3.5	−0.6 to −3.5	−0.6 to −3.5	−0.6 to −3.5	−0.6 to −3.5	−0.6 to −3.5
Pixel size (Å)	0.685	0.685	0.685	0.685	0.685	0.685	0.685	0.685
Symmetry imposed	C1	C1	C1	C1	C1	C1	C1	C1
Initial particle images (no.)	3,584,040	3,584,040	3,584,040	3,584,040	3,584,040	3,584,040	3,584,040	3,584,040
Final particle images (no.)	184,848	105,157	79,691	242,965	112,776	71,651	288,915	348,646
Map resolution (Å)	2.8	3.0	3.2	3.3	3.5	3.6	3.3	3.2
FSC threshold	0.143	0.143	0.143	0.143	0.143	0.143	0.143	0.143
Map resolution range(Å)	2.5-5.8	2.5-5.8	2.5-6.9	2.5-4.7	2.8-5.8	3.0-6.9	2.5-5.8	2.5-4.7
Refinement
Initial model used		5VFS						5VFO(partly)
Model resolution (Å)	3.2	3.4	3.8	3.5	3.7	3.8	3.4	3.4
FSC threshold	0.5	0.5	0.5	0.5	0.5	0.5	0.5	0.5
Model resolution range (Å)	2.5-5.8	2.5-5.8	2.5-6.9	2.5-4.7	2.8-5.8	3.0-6.9	2.5-5.8	2.5-4.7
Map sharpening B factor (Å2)	−50	−50	−46	−35	−30	−50	−35	−30
Model composition
Non-hydrogen atoms	104400	104400	104400	105147	104415	103777	105336	105244
Protein residues	13180	13180	13180	13400	13305	13328	13403	13395
Ligands	11	11	11	10	6	5	10	10
B factors (Å2)
Protein	98.31	120.31	195.53	117.64	220.54	280.72	187.13	197.24
Ligand	89.88	112.21	191.81	118.98	217.88	261.40	181.50	192.26
R.m.s. deviations
Bond lengths (Å)	0.007	0.01	0.012	0.006	0.005	0.004	0.007	0.007
Bond angles (°)	0.925	1.075	1.013	1.025	0.871	0.901	1.266	1.187
Validation
MolProbity score	1.5	1.69	1.77	1.83	1.65	1.71	1.86	1.88
Clashscore	2.69	2.91	5.02	5.63	4.00	4.2	5.87	5.83
Poor rotamers (%)	0.34	0.42	0.42	0.66	0.28	0.19	0.45	0.5
Ramachandran plot
Favored (%)	93.07	92.45	91.59	90.83	92.56	91.46	90.13	89.61
Allowed (%)	6.76	7.33	8.15	8.83	7.21	8.31	9.58	10.09
Disallowed (%)	0.17	0.22	0.26	0.34	0.23	0.23	0.29	0.3